Support Vector Machines in Classification and Regression Problems

117 σ.Η μηχανική μάθηση έχει ως στόχο τη δημιουργία αλγορίθμων ικανών να βελτιώνουν την απόδοση τους, αξιοποιώντας προγενέστερη γνώση και εμπειρία, με σκοπό την εξαγωγή χρήσιμων συμπερασμάτων και την περιγραφή φαινομένων, μέσω της επεξεργασίας δεδομένων τεράστιου, πολλές φορές, όγκου. Το ζητούμενο στην περίπτωση της επιβλεπόμενης μάθησης είναι η κατασκευή ενός μοντέλου που αναπαριστά τη γνώστη που αποκτήθηκε μέσω της εμπειρίας και το οποίο στη συνέχεια χρησιμοποιείται για την αξιολόγηση νέων παρατηρήσεων. Μία από τις πιο οικείες μεθόδους περιγραφής φαινομένων είναι η ταξινόμηση, η ένταξη δηλαδή κάθε παρατήρησης σε μία ομάδα, από ένα πεπερασμένο πλήθος υποψήφιων ομάδων. Η παρούσα εργασία επικεντρώνεται στην παρουσίαση ενός πολύ διαδεδομένου αλγόριθμου ταξινόμησης, προερχόμενου από τον τομέα της μηχανικής μάθησης, με όνομα «Μηχανή Διανυσματικής Υποστήριξης» (Support Vector Machine - SVM). Η ανάπτυξη του θεωρητικού υπόβαθρου του αλγόριθμου παρουσιάζεται σταδιακά, ώστε να γίνει κατανοητή από τον αναγνώστη όλη η διαδρομή. Πιο συγκεκριμένα, το πρώτο κεφάλαιο αποτελεί μια εισαγωγή στους αλγόριθμους εξόρυξης δεδομένων (Data Mining) και σε σχετικές εφαρμογές αυτών. Στο δεύτερο κεφάλαιο παρουσιάζονται οι θεμελιώδεις έννοιες που απαιτούνται για την κατανόηση των SVMs. Στο τρίτο και στο τέταρτο κεφάλαιο γίνεται μία λεπτομερής αναφορά στις Μηχανές Διανυσματικής Υποστήριξης και στην Παλινδρόμηση με SVM, αντίστοιχα. Στη συνέχεια, στο πέμπτο κεφάλαιο παρουσιάζουμε τις μεθόδους αξιολόγησης του μοντέλου ενώ στο έκτο κεφάλαιο κάνουμε μία μικρή αναφορά στην επιλογή χαρακτηριστικών με SVM. Στο έβδομο και τελευταίο κεφάλαιο παρουσιάζουμε τρεις εφαρμογές καθώς και την ερμηνεία των αντίστοιχων αποτελεσμάτων, με σκοπό να αξιολογήσουμε τη γνώση που αποκτήσαμε.The aim of machine learning is to develop algorithms capable of improving their own performance, exploiting existing data, stored in huge databases, in order to discover knowledge and interpret several phenomena. Supervised learning aims in creating a model that takes into account the knowledge adapted by experience, and then uses it for evaluating new observations. One of the most common methods for describing phenomena is through classification. Where a particular object is classified to one of several available classes of objects. The presentation thesis focuses on one of the most promising classification algorithms in the field of machine learning, the «The Support Vector Machine» (SVM). The presentation of the theoretical foundation advances gradually, starting from the most intuitive classification algorithm and reaching up to the optimized approach of SVM, so that it΄s easier for the reader to follow. More specifically, the first chapter is an introduction to data mining algorithms and some related applications. The second chapter presents the fundamental concepts required for an understanding of SVMs. In the third and fourth chapter, there is a detailed report on Support Vector Machines and Regression with SVM, respectively. Then, the fifth chapter presents the evaluation methods of the model while in the sixth chapter a short reference to the feature selection with SVM in made. In the seventh and final chapter three applications and the interpretation of the corresponding results are presented, thus we are able to evaluate the knowledge gained.Δανάη Π. Γιαννούλ

The actin binding proteins cortactin and HS1 are dispensable for platelet actin nodule and megakaryocyte podosome formation

A dynamic, properly organised actin cytoskeleton is critical for the production and haemostatic function of platelets. The Wiskott Aldrich Syndrome protein (WASp) and Actin-Related Proteins 2 & 3 Complex (Arp2/3 complex) are critical mediators of actin polymerisation and organisation in many cell types. In platelets and megakaryocytes, these proteins have been shown to be important for proper platelet production and function. The cortactin family of proteins (Cttn & HS1) are known to regulate WASp-Arp2/3-mediated actin polymerisation in other cell types and so here we address the role of these proteins in platelets using knockout mouse models. We generated mice lacking Cttn and HS1 in the megakaryocyte/platelet lineage. These mice had normal platelet production, with platelet number, size and surface receptor profile comparable to controls. Platelet function was also unaffected by loss of Cttn/HS1 with no differences observed in a range of platelet function assays including aggregation, secretion, spreading, clot retraction or tyrosine phosphorylation. No effect on tail bleeding time or in thrombosis models was observed. In addition, platelet actin nodules, and megakaryocyte podosomes, actin-based structures known to be dependent on WASp and the Arp2/3 complex, formed normally. We conclude that despite the importance of WASp and the Arp2/3 complex in regulating F-actin dynamics in many cells types, the role of cortactin in their regulation appears to be fulfilled by other proteins in platelets

Adipocyte lipid synthesis coupled to neuronal control of thermogenic programming

BACKGROUND: The de novo biosynthesis of fatty acids (DNL) through fatty acid synthase (FASN) in adipocytes is exquisitely regulated by nutrients, hormones, fasting, and obesity in mice and humans. However, the functions of DNL in adipocyte biology and in the regulation of systemic glucose homeostasis are not fully understood. METHODS and RESULTS: Here we show adipocyte DNL controls crosstalk to localized sympathetic neurons that mediate expansion of beige/brite adipocytes within inguinal white adipose tissue (iWAT). Induced deletion of FASN in white and brown adipocytes of mature mice (iAdFASNKO mice) enhanced glucose tolerance, UCP1 expression, and cAMP signaling in iWAT. Consistent with induction of adipose sympathetic nerve activity, iAdFASNKO mice displayed markedly increased neuronal tyrosine hydroxylase (TH) and neuropeptide Y (NPY) content in iWAT. In contrast, brown adipose tissue (BAT) of iAdFASNKO mice showed no increase in TH or NPY, nor did FASN deletion selectively in brown adipocytes (UCP1-FASNKO mice) cause these effects in iWAT. CONCLUSIONS: These results demonstrate that downregulation of fatty acid synthesis via FASN depletion in white adipocytes of mature mice can stimulate neuronal signaling to control thermogenic programming in iWAT

Pitfalls in Quantitative Myocardial PET Perfusion I: Myocardial Partial Volume Correction

BACKGROUND: PET quantitative myocardial perfusion requires correction for partial volume loss due to one-dimensional LV wall thickness smaller than scanner resolution. METHODS: We aimed to assess accuracy of risk stratification for death, MI, or revascularization after PET using partial volume corrections derived from two-dimensional ACR and three-dimensional NEMA phantoms for 3987 diagnostic rest-stress perfusion PETs and 187 MACE events. NEMA, ACR, and Tree phantoms were imaged with Rb-82 or F-18 for size-dependent partial volume loss. Perfusion and Coronary Flow Capacity were recalculated using different ACR- and NEMA-derived partial volume corrections compared by Kolmogorov-Smirnov statistics to standard perfusion metrics with established correlations with MACE. RESULTS: Partial volume corrections based on two-dimensional ACR rods (two equal radii) and three-dimensional NEMA spheres (three equal radii) over estimate partial volume corrections, quantitative perfusion, and Coronary Flow Capacity by 50% to 150% over perfusion metrics with one-dimensional partial volume correction, thereby substantially impairing correct risk stratification. CONCLUSIONS: ACR (2-dimensional) and NEMA (3-dimensional) phantoms overestimate partial volume corrections for 1-dimensional LV wall thickness and myocardial perfusion that are corrected with a simple equation that correlates with MACE for optimal risk stratification applicable to most PET-CT scanners for quantifying myocardial perfusion

Endothelial Mitogen-Activated Protein Kinase Kinase Kinase Kinase 4 Is Critical for Lymphatic Vascular Development and Function

The molecular mechanisms underlying lymphatic vascular development and function are not well understood. Recent studies have suggested a role for endothelial cell (EC) mitogen-activated protein kinase kinase kinase kinase 4 (Map4k4) in developmental angiogenesis and atherosclerosis. Here, we show that constitutive loss of EC Map4k4 in mice causes postnatal lethality due to chylothorax, suggesting that Map4k4 is required for normal lymphatic vascular function. Mice constitutively lacking EC Map4k4 displayed dilated lymphatic capillaries, insufficient lymphatic valves, and impaired lymphatic flow; furthermore, primary ECs derived from these animals displayed enhanced proliferation compared with controls. Yeast 2-hybrid analyses identified the Ras GTPase-activating protein Rasa1, a known regulator of lymphatic development and lymphatic endothelial cell fate, as a direct interacting partner for Map4k4. Map4k4 silencing in ECs enhanced basal Ras and extracellular signal-regulated kinase (Erk) activities, and primary ECs lacking Map4k4 displayed enhanced lymphatic EC marker expression. Taken together, these results reveal that EC Map4k4 is critical for lymphatic vascular development by regulating EC quiescence and lymphatic EC fate

MAP4K4 impairs energy metabolism in endothelial cells and promotes insulin resistance in obesity

The blood vasculature responds to insulin, influencing hemodynamic changes in the periphery, which promotes tissue nutrient and oxygen delivery and thus metabolic function. The lymphatic vasculature regulates fluid and lipid homeostasis, and impaired lymphatic function can contribute to atherosclerosis and obesity. Recent studies have suggested a role for endothelial cell (EC) Mitogen activated protein kinase kinase kinase kinase 4 (Map4k4) in developmental angiogenesis and lymphangiogenesis as well as atherosclerosis. Here, we show that inducible EC Map4k4 deletion in adult mice ameliorates metabolic dysfunction in obesity despite the development of chylous ascites and a concomitant striking increase in adipose tissue lymphocyte content. Despite these defects, animals lacking endothelial Map4k4 were protected from skeletal muscle microvascular rarefaction in obesity, and primary ECs lacking Map4k4 displayed reduced senescence and increased metabolic capacity. Thus, endothelial Map4k4 has complex and opposing functions in the blood and lymphatic endothelium post-development. Whereas blood endothelial Map4k4 promotes vascular dysfunction and impairs glucose homeostasis in adult animals, lymphatic endothelial Map4k4 is required to maintain lymphatic vascular integrity and regulate immune cell trafficking in obesity

Inducible Deletion of Protein Kinase Map4k4 in Obese Mice Improves Insulin Sensitivity in Liver and Adipose Tissues

Studies in vitro suggest that mitogen-activated protein kinase kinase kinase kinase 4 (Map4k4) attenuates insulin signaling, but confirmation in vivo is lacking since Map4k4 knockout is lethal during embryogenesis. We thus generated mice with floxed Map4k4 alleles and a tamoxifen-inducible Cre/ERT2 recombinase under the control of the ubiquitin C promoter to induce whole-body Map4k4 deletion after these animals reached maturity. Tamoxifen administration to these mice induced Map4k4 deletion in all tissues examined, causing decreased fasting blood glucose concentrations and enhanced insulin signaling to AKT in adipose tissue and liver but not in skeletal muscle. Surprisingly, however, mice generated with a conditional Map4k4 deletion in adiponectin-positive adipocytes or in albumin-positive hepatocytes displayed no detectable metabolic phenotypes. Instead, mice with Map4k4 deleted in Myf5-positive tissues, including all skeletal muscles tested, were protected from obesity-induced glucose intolerance and insulin resistance. Remarkably, these mice also showed increased insulin sensitivity in adipose tissue but not skeletal muscle, similar to the metabolic phenotypes observed in inducible whole-body knockout mice. Taken together, these results indicate that (i) Map4k4 controls a pathway in Myf5-positive cells that suppresses whole-body insulin sensitivity and (ii) Map4k4 is a potential therapeutic target for improving glucose tolerance and insulin sensitivity in type 2 diabetes

Inter-familial and intra-familial phenotypic variability in three Sicilian families with Anderson-Fabry disease.

Abstract BACKGROUND: Anderson-Fabry disease (AFD) is an inborn lysosomal enzymopathy resulting from the deficient or absent activity of the lysosomal exogalactohydrolase, α-galactosidase A. This deficiency, results in the altered metabolism of glycosphingolipids which leads to their accumulation in lysosomes, thus to cellular and vascular dysfunction. To date, numerous mutations (according to recent data more than 1000 mutations) have been reported in the GLA intronic and exonic mutations. Traditionally, clinical manifestations are more severe in affected hemizygous males than in females. Nevertheless, recent studies have described severe organ dysfunction in women. THE AIM OF THE STUDY: This study reports clinical, biochemical, and molecular findings of the members of three Sicilian families. The clinical history of these patients highlights a remarkable interfamilial and intrafamilial phenotypic variability which characterizes Fabry disease relative to target organs and severity of clinical manifestations. DISCUSSION: Our findings, in agreement with previous data, report a little genotype-phenotype correlation for the disease, suggesting that the wide phenotypic variability of Anderson-Fabry disease is not completely ascribable to different gene mutations but other factors and mechanisms seem to be involved in the pathogenesis and clinical expression of the disease. Moreover, this study emphasies the importance of pedigree analysis in the family of each proband for identifying other possibly affected relatives

Endothelial protein kinase MAP4K4 promotes vascular inflammation and atherosclerosis

Signalling pathways that control endothelial cell (EC) permeability, leukocyte adhesion and inflammation are pivotal for atherosclerosis initiation and progression. Here we demonstrate that the Sterile-20-like mitogen-activated protein kinase kinase kinase kinase 4 (MAP4K4), which has been implicated in inflammation, is abundantly expressed in ECs and in atherosclerotic plaques from mice and humans. On the basis of endothelial-specific MAP4K4 gene silencing and gene ablation experiments in Apoe(-/-) mice, we show that MAP4K4 in ECs markedly promotes Western diet-induced aortic macrophage accumulation and atherosclerotic plaque development. Treatment of Apoe(-/-) and Ldlr(-/-) mice with a selective small-molecule MAP4K4 inhibitor also markedly reduces atherosclerotic lesion area. MAP4K4 silencing in cultured ECs attenuates cell surface adhesion molecule expression while reducing nuclear localization and activity of NFkappaB, which is critical for promoting EC activation and atherosclerosis. Taken together, these results reveal that MAP4K4 is a key signalling node that promotes immune cell recruitment in atherosclerosis